yes, i have integrated almost all the javascript charts with cognos 10.1 . i was able to use them in interactive reports, in scheduled emails as an HTML/MHT attachment(much lighter than active reports).They look awecome in cognos and sometimes much faster than even in built cognos charts.
Obviously it takes more time to integrate/create/code an amChart in cognos than regular COGNOS chart.there are some issues related to drill thru ,pallette options,visual effects and other integration aspects  .